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- PDB-1xux: Structural rationalization of a large difference in RNA affinity ... -

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Basic information

Entry
Database: PDB / ID: 1xux
TitleStructural rationalization of a large difference in RNA affinity despite a small difference in chemistry between two 2'-O-modified nucleic acid analogs
ComponentsDNA (5'-D(*GP*CP*GP*TP*AP*(NMS)P*AP*CP*GP*C)-3')
KeywordsDNA / RNA mimetic methylamino amide analog
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsPattanayek, R. / Sethaphong, L. / Pan, C. / Prhavc, M. / Prakash, T.P. / Manoharan, M. / Egli, M.
CitationJournal: J.Am.Chem.Soc. / Year: 2004
Title: Structural rationalization of a large difference in RNA affinity despite a small difference in chemistry between two 2'-O-modified nucleic acid analogues.
Authors: Pattanayek, R. / Sethaphong, L. / Pan, C. / Prhavc, M. / Prakash, T.P. / Manoharan, M. / Egli, M.
History
DepositionOct 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*GP*CP*GP*TP*AP*(NMS)P*AP*CP*GP*C)-3')
B: DNA (5'-D(*GP*CP*GP*TP*AP*(NMS)P*AP*CP*GP*C)-3')
C: DNA (5'-D(*GP*CP*GP*TP*AP*(NMS)P*AP*CP*GP*C)-3')
D: DNA (5'-D(*GP*CP*GP*TP*AP*(NMS)P*AP*CP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)12,5284
Polymers12,5284
Non-polymers00
Water5,350297
1
A: DNA (5'-D(*GP*CP*GP*TP*AP*(NMS)P*AP*CP*GP*C)-3')
B: DNA (5'-D(*GP*CP*GP*TP*AP*(NMS)P*AP*CP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)6,2642
Polymers6,2642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA (5'-D(*GP*CP*GP*TP*AP*(NMS)P*AP*CP*GP*C)-3')
D: DNA (5'-D(*GP*CP*GP*TP*AP*(NMS)P*AP*CP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)6,2642
Polymers6,2642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.057, 44.606, 44.106
Angle α, β, γ (deg.)90.00, 99.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain
DNA (5'-D(*GP*CP*GP*TP*AP*(NMS)P*AP*CP*GP*C)-3')


Mass: 3132.083 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: synthetically created
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.39 Å3/Da / Density % sol: 71.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1mM 10mer, 40mM sodium cacodylate, 12 mM spermine 4HCl, 80mM potassium chloride, 10% MPD, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.96297 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96297 Å / Relative weight: 1
ReflectionResolution: 1.3→30 Å / Num. all: 23065 / Num. obs: 23065 / % possible obs: 90.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.044
Reflection shellResolution: 1.3→1.38 Å / Redundancy: 13.1 % / Rmerge(I) obs: 0.073 / Num. unique all: 2093 / % possible all: 49.8

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
EPMRphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DPL

1dpl


Resolution: 1.3→30 Å / Cross valid method: throughtout / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.194 1150 random
Rwork0.127 --
all0.127 21902 -
obs0.127 21902 -
Refinement stepCycle: LAST / Resolution: 1.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 854 0 304 1158
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.022

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